I am currently involved in a collaborative project aimed at the study of nonconventional intermolecular interactions in solution, by means of molecular dynamics free energy calculations. In particular, we have investigated the nature of pi-pi and pi-cation noncovalent interactions in proteins, carrying out free energy simulations on prototypical systems in an aqueous solution. The so-called pi-cation interactions are of utmost importance in a variety of biological receptors especially those that bind neurotransmitters, like acetylcholine, but the substantial polarization effects observed in these systems preclude any accurate description of such interactions by means of minimalist two-body empirical force fields. We have proposed a simple and economic way to circumvent this shortcoming, by introducing a specific short-range term to the Amber potential energy function, and we have tested this approach on the archetypical toluene-ammonium solvated complex. Pi-pi interactions are equally important as they are believed to play a significant role in the folding and complexation behavior of biopolymers. We have compared thoroughly the orientational preferences of the benzene and the toluene dimers, as prototypes of the phenylalanine-phenylalanine interactions in proteins. For all these investigations, use was made of the University of California, San Francisco Computer Graphics Laboratory facilities to visualize configurations and trajectories.